[Loris-dev] Import mri - scripts
Cecile Madjar
cecile.madjar at mcin.ca
Thu Sep 26 10:07:21 EDT 2019
Hi Sotirios,
Sorry to hear you are having issues with the memory. I think most of our
VMs are set up with 4GB of RAM so with 4GB you should be fine.
Hope this helps!
Cécile
On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> Hi,
>
> about that dicom that had that insertion error it's about 30mb and when it
> is being processed the ram is being drastically increased from 2gb to 3.28
> and then the whole virtual machine is frozen. What is the recommended size
> of ram for using Loris?
>
> Thanks
>
> [image: image.png]
>
>
> Στις Τρί, 24 Σεπ 2019 στις 11:24 μ.μ., ο/η Cecile Madjar <
> cecile.madjar at mcin.ca> έγραψε:
>
>> Hi Sotirios,
>>
>> Glad to see that the StudyUID problem was fixed!
>>
>> For the delete script issue, if you are absolutely certain that no
>> processes are run for that uploadID, you can update the mri_upload table
>> and set the column Inserting to 0 instead of 1 for that uploadID. It
>> looks like for some reason the scripts did not update this field when it
>> stopped the insertion. Not sure why that would be the case though.
>> Note: only do that update if you are certain that there is no processing
>> happening.
>>
>> Hope this helps!
>>
>>
>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> about the Dicoms i reported that didn't have a StudyID they actually do
>>>
>>> [image: image.png]
>>>
>>>
>>> [image: image.png]
>>>
>>> I thought that this might be a permission because "w" was missing at the
>>> group. After using chmod -R 775 only 102809579 passed, but with no mnic
>>> files. Also now i have this error
>>>
>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$
>>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>> Cannot delete upload 34: the MRI pipeline is currently processing it.
>>>
>>> How can solve this?
>>>
>>> Thanks
>>>
>>>
>>> Στις Τρί, 24 Σεπ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>>> Hi,
>>>>
>>>> Here is our auto dicom uploading python script:
>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>
>>>> To give you a brief idea:
>>>> Per folder it will:
>>>> 1) Delete all the .bak files
>>>> 2) Locate .dcm files and update the Patient header
>>>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min,
>>>> TE_max parameters of T1 protocol and do an update at the mri_protocol table
>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>> For some reason some files are missing SeriesDescription/ProtocolName
>>>>
>>>> In total i have 7 folders
>>>>
>>>> [image: image.png]
>>>>
>>>> 3/7 passed
>>>>
>>>> [image: image.png]
>>>>
>>>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE
>>>> GADO", but my script didn't output a TE of 17 nowhere and i find that weird
>>>> since Loris detects the SeriesDescription.
>>>> [image: image.png]
>>>>
>>>>
>>>> Now about the 4/7 that didn't passed
>>>>
>>>> 102327840 and 102809579 outputs "The target directory does not contain
>>>> a single DICOM file.", therefore they are missing their StudyUID
>>>>
>>>> 102506134 has 2 studyuid "You can't use it with data from multiple
>>>> studies."
>>>>
>>>> and 102761034 "No data could be converted into valid MINC files.
>>>> localizer, scout will not be considered!" What is this?
>>>>
>>>> If i wanted to force the insertion of 102327840, 102809579 and
>>>> 102506134 can i just pass a flag parameter to
>>>> batch_uploads_imageuploader.pl? or modify imaging_upload_file.pl?
>>>>
>>>> Thank you,
>>>>
>>>> Sotirios
>>>>
>>>> PS
>>>>
>>>> To diagnose a folder search the name of the folder at dicom_output.txt.
>>>>
>>>> Στις Παρ, 20 Σεπ 2019 στις 4:54 μ.μ., ο/η Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>> Glad to hear about your progress.
>>>>>
>>>>> Yes, the script you used to delete imaging data is fully documented
>>>>> here
>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md>
>>>>> -- let us know if you didn't find the answers you were looking for there.
>>>>> (Is it possible the null row in *mri_scanner* seen in your database
>>>>> management software is a visual placeholder for you as the user? I'm not
>>>>> sure why a scanner would ever be registered with ID='0' as your screenshot
>>>>> showed.)
>>>>>
>>>>> Best,
>>>>> Christine
>>>>>
>>>>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> I fixed it with this
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>> Στις Παρ, 20 Σεπ 2019 στις 4:37 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I tried to create a new candidate using the API, is there something
>>>>>>> wrong with the structure? why did i receive a 500 internal error? In the
>>>>>>> loris-error log it state that there is something wrong with token, but i
>>>>>>> verfied that the type of the token is a string.
>>>>>>>
>>>>>>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client
>>>>>>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1
>>>>>>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>> null given, called in
>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>> defined in
>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>> SinglePointLogin->authenticate()\n#2
>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in
>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>
>>>>>>> [image: image.png]
>>>>>>>
>>>>>>> Στις Παρ, 20 Σεπ 2019 στις 2:39 μ.μ., ο/η Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> Is there a way also to delete candidates? Just to let you know what
>>>>>>>> i did to clear candidates, because maybe i may have missed dependencies.
>>>>>>>>
>>>>>>>> First i deleted all their uploads
>>>>>>>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to
>>>>>>>> omit the backup file ? )
>>>>>>>>
>>>>>>>> Afterwards i had some scanner candidates, so i deleted all the
>>>>>>>> entries from mri_scanner except that i couldn't delete this entry with the
>>>>>>>> 0 ID.
>>>>>>>>
>>>>>>>> [image: image.png]
>>>>>>>>
>>>>>>>>
>>>>>>>> Lastly i deleted the session and then the candidate table.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Στις Πέμ, 19 Σεπ 2019 στις 7:57 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> We recommend that you use our existing tools for creating new
>>>>>>>>> candidates - either the LORIS API or if you are using a PHP script, by
>>>>>>>>> calling the Candidate class's createNew()
>>>>>>>>> <https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200>function.
>>>>>>>>> These will create the necessary records for you. (It's not recommended to
>>>>>>>>> make direct modifications to mysql database tables in your script, if I
>>>>>>>>> understand you.)
>>>>>>>>>
>>>>>>>>> The CandID should be a randomized 6 digit randomized ID, and there
>>>>>>>>> are multiple reasons for this.
>>>>>>>>> You can use the PSCID for project-specific IDs and the External ID
>>>>>>>>> field in the candidate table can also be used for any values you like.
>>>>>>>>> Additionally, any number of custom IDs can be added in parallel -
>>>>>>>>> these are entered/visible in the Candidate Information module and added in
>>>>>>>>> the back-end as candidate parameters.
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> Christine
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> We are building a script that will auto insert the candidates
>>>>>>>>>> based on their ExternalID. We would like to know whethere when we are
>>>>>>>>>> creating a new profile in the candidate table, if we also have to insert a
>>>>>>>>>> new record at another table? Furthermore is there a problem that in our
>>>>>>>>>> case CandID won't be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 5:38 μ.μ., ο/η Melanie Legault, Mrs <
>>>>>>>>>> melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> That would normally be the case but the numeric part of the
>>>>>>>>>>> PSCID get paded with 0 on the left.
>>>>>>>>>>>
>>>>>>>>>>> Ex. for sequential ID made of center ID of `ABC` plus 4
>>>>>>>>>>> numerical char with a min value of 1, the sequence would be:
>>>>>>>>>>>
>>>>>>>>>>> ABC0001
>>>>>>>>>>> ABC0002
>>>>>>>>>>> ...
>>>>>>>>>>> ABC0010
>>>>>>>>>>> ...
>>>>>>>>>>>
>>>>>>>>>>> thus sorting them ascending will always get the latest value
>>>>>>>>>>> generated as the max value.
>>>>>>>>>>>
>>>>>>>>>>> Mélanie
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------
>>>>>>>>>>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>>>>>>>>>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>
>>>>>>>>>>> I see, although the PSCID value is varchar(255), it must be
>>>>>>>>>>> stored within a specific length of characters. Otherwise if we were to sort
>>>>>>>>>>> strings with different lengths the result would not be sorted correctly (
>>>>>>>>>>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Στις Παρ, 13 Σεπ 2019 στις 4:52 μ.μ., ο/η Melanie Legault, Mrs <
>>>>>>>>>>> melanie.legault2 at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hello Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> There is no `last value` stored anywhere.
>>>>>>>>>>> The code simply look for the PSCID with the max value and
>>>>>>>>>>> increase that value by 1 in order to generate the next PSCID.
>>>>>>>>>>>
>>>>>>>>>>> Hope this info help.
>>>>>>>>>>>
>>>>>>>>>>> Mélanie Legault | Software developer | Faculty of Medicine | McGill
>>>>>>>>>>> University
>>>>>>>>>>> 3801 University, Montréal, QC H3A 2B4
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------
>>>>>>>>>>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> how does Loris determine the next available PSCID value for a
>>>>>>>>>>> new candidate?
>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization e.x in
>>>>>>>>>>> the default case the PSCID is sequential, but where do we store the last
>>>>>>>>>>> value for the sequential sequence?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Στις Τρί, 10 Σεπ 2019 στις 4:00 π.μ., ο/η Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> the parameters in the mri_protocol you have assigned are global
>>>>>>>>>>> standard? or were assigned after trial and error?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 10:11 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Given you have done the initial setup of your tables to match
>>>>>>>>>>> your intended protocol/parameters according to instructions --
>>>>>>>>>>> the Troubleshooting guide documentation recommends
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes>
>>>>>>>>>>> re-running the pipeline (and first deleting prior uploads).
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> *if i were to change their status to resolve what would happen?
>>>>>>>>>>>
>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 5:12 μ.μ., ο/η Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> I noticed that i can view the mnics at the brainbrowser from the
>>>>>>>>>>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/
>>>>>>>>>>> if i were to click their issue to resolve what would happend? would they
>>>>>>>>>>> appear in the dicom_archive view too? ).
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Στις Κυρ, 8 Σεπ 2019 στις 4:17 μ.μ., ο/η Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> The defaut values of the schema exists in my local database. If
>>>>>>>>>>> i adjust the default values of TR_min and TE_min the mincs will be uploaded?
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 5:48 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Is it possible that you haven't set up your mri_protocol table
>>>>>>>>>>> ? (and mri_scan_type table too, for additional types of scans)
>>>>>>>>>>>
>>>>>>>>>>> Like the psc table, this is a pre-requisite for the Imaging
>>>>>>>>>>> insertion setup : See the install/setup documentation :
>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>
>>>>>>>>>>> To add new rows, just use MySQL insert statements. You can
>>>>>>>>>>> adapt the insert statements which load the default table values --> e.g.
>>>>>>>>>>> Here on GitHub :
>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>> (see also the mri_scan_type table)
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> I see that i can edit the values but not how to insert new rows.
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> If i choose Inserted with flag then will the minc be inserted?
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:21 π.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>
>>>>>>>>>>> For the MRI Violations module, the screenshot is enough.
>>>>>>>>>>>
>>>>>>>>>>> It says "could not identify scan type", which we knew already.
>>>>>>>>>>> Did you click on the link on those words?
>>>>>>>>>>>
>>>>>>>>>>> It will take you to the next page of the module, showing for
>>>>>>>>>>> each scan what the scan parameters were, and will also show for comparison
>>>>>>>>>>> what's stored in your *mri_protocol* table.
>>>>>>>>>>> Compare these values to find which parameter was not correct
>>>>>>>>>>> according to your *mri_protocol* table scan type definitions.
>>>>>>>>>>>
>>>>>>>>>>> You may end up broadening your mri_protocol value ranges (e.g.
>>>>>>>>>>> TR, TE) for scans.
>>>>>>>>>>> This can be done in the front-end, by editing the database table
>>>>>>>>>>> directly in the same subpage of the MRI Violations module.
>>>>>>>>>>>
>>>>>>>>>>> The MRI Violations module features are explained in more detail
>>>>>>>>>>> in the Help text for this module inside LORIS (click the ["?"] icon in the
>>>>>>>>>>> menu bar.)
>>>>>>>>>>>
>>>>>>>>>>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md>
>>>>>>>>>>> : no MINCs inserted- violated scans
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> looks like my previous email's attachment wasn't delivered due
>>>>>>>>>>> to security reasons, i uploaded my file at google drive
>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>
>>>>>>>>>>> Στις Σάβ, 7 Σεπ 2019 στις 3:02 π.μ., ο/η Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> From Dicat's view seems that dcmodify worked in both cases
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> For the mri_violations i attached the .html output from
>>>>>>>>>>> webbrowser, so that you can check the filelds easier.
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Στις Παρ, 6 Σεπ 2019 στις 7:49 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios --
>>>>>>>>>>> Great, sounds like more progress.
>>>>>>>>>>>
>>>>>>>>>>> About the dcmodify command -- I'm not sure why you're getting an
>>>>>>>>>>> Endian warning. (it's a warning not an error, correct?)
>>>>>>>>>>> To clarify -- Were the DICOM headers (PatientName) all
>>>>>>>>>>> successfully relabelled, after the command ran?
>>>>>>>>>>>
>>>>>>>>>>> You can use also our DICAT tool (https://github.com/aces/DICAT) to
>>>>>>>>>>> verify and/or update local DICOM headers -- though your dcmodify command is
>>>>>>>>>>> a great and fast solution for bulk header updates.
>>>>>>>>>>>
>>>>>>>>>>> If you're concerned about fields being changed (e.g.
>>>>>>>>>>> "(2001,105f)" from the warning message) - you can also dcmdump a DICOM
>>>>>>>>>>> slice before and look at these fields specifically.
>>>>>>>>>>> It's also not a bad "sanity check" to backup your DICOMS
>>>>>>>>>>> before/after running dcmodify, and use dcmdump on each version to diff the
>>>>>>>>>>> outputs -- this will pinpoint what changed.
>>>>>>>>>>>
>>>>>>>>>>> Re the protocol violation -- AcquisitionProtocol not recognized
>>>>>>>>>>> or unknown : this means your scans did not match what is stored in your
>>>>>>>>>>> mri_protocol table.
>>>>>>>>>>> Check the MRI Violations front-end module -- can you see why
>>>>>>>>>>> they didn't match?
>>>>>>>>>>> Send us an example, in addition to the contents of the
>>>>>>>>>>> mri_protocol table, if you can't find the source of the mismatch.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Here is the psc table
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> I created 2 candidates profiles through the interface
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> then runned dcmodify command to a dicom file
>>>>>>>>>>>
>>>>>>>>>>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>
>>>>>>>>>>> and got those warning: is this okay?
>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>> W: Found element (2005,1402) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>> W: Found element (2005,140f) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>> W: Found element (2001,105f) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>> W: Found element (2005,1083) with VR UN and undefined length,
>>>>>>>>>>> reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
>>>>>>>>>>>
>>>>>>>>>>> dcmodify at another Dicom didn't show warnings. Below you can
>>>>>>>>>>> see the execution for the second dicom. Mnics could not be inserted due to
>>>>>>>>>>> AcquisitionProtocol being unknown.
>>>>>>>>>>>
>>>>>>>>>>> Running now the following command:
>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/imaging_upload_file.pl
>>>>>>>>>>> -profile prod -upload_id 12 /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>
>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name
>>>>>>>>>>> '__MACOSX' -delete
>>>>>>>>>>>
>>>>>>>>>>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>>>>>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>> Target: /data/loris/data/tarchive
>>>>>>>>>>>
>>>>>>>>>>> Testing for database connectivity.
>>>>>>>>>>> Database is available.
>>>>>>>>>>>
>>>>>>>>>>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>
>>>>>>>>>>> You are creating a tar with the following command:
>>>>>>>>>>>
>>>>>>>>>>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> getting md5sums and gzipping!!
>>>>>>>>>>>
>>>>>>>>>>> * Taken from dir :
>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>> * Archive target location :
>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>> * Name of creating host : 127.0.1.1
>>>>>>>>>>> * Name of host OS : Linux
>>>>>>>>>>> * Created by user : lorisadmin
>>>>>>>>>>> * Archived on : 2019-09-06 18:36:50
>>>>>>>>>>> * dicomSummary version : 1
>>>>>>>>>>> * dicomTar version : 1
>>>>>>>>>>> * md5sum for DICOM tarball :
>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>> * md5sum for complete archive :
>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>
>>>>>>>>>>> Adding archive info into database
>>>>>>>>>>>
>>>>>>>>>>> Removing temporary files from target location
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Done adding archive info into database
>>>>>>>>>>>
>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl
>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>> -uploadID 12 -verbose
>>>>>>>>>>> md5sum
>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> candidate id 602102
>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>
>>>>>>>>>>> Number of MINC files that will be considered for inserting into
>>>>>>>>>>> the database: 2
>>>>>>>>>>>
>>>>>>>>>>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> candidate id 602102
>>>>>>>>>>>
>>>>>>>>>>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> PSCID is: DCC0001
>>>>>>>>>>> CandID id: 602102
>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>> candidate id 602102
>>>>>>>>>>>
>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>
>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>> cat /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>
>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>
>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>
>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>
>>>>>>>>>>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>
>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>
>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>
>>>>>>>>>>> --> The minc file cannot be registered since the
>>>>>>>>>>> AcquisitionProtocol is unknown
>>>>>>>>>>>
>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 10:46 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios:
>>>>>>>>>>>
>>>>>>>>>>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>> *delete_imaging_upload* script --
>>>>>>>>>>> details here:
>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>
>>>>>>>>>>> What's in your *psc* table? (Is it properly populated? This is
>>>>>>>>>>> a pre-requisite to loading imaging data.
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>> )
>>>>>>>>>>> The foreign key constraint error on the candidate record is
>>>>>>>>>>> curious.
>>>>>>>>>>>
>>>>>>>>>>> There are also a few options for creating candidates when
>>>>>>>>>>> inserting imaging data:
>>>>>>>>>>>
>>>>>>>>>>> -- Method 1 : in 2 steps with the API then DICOM insertion
>>>>>>>>>>> pipeline
>>>>>>>>>>>
>>>>>>>>>>> a. via the LORIS API -- Create the candidates (and visits,
>>>>>>>>>>> optionally I think)
>>>>>>>>>>> How to:
>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>>>
>>>>>>>>>>> Then as a second step:
>>>>>>>>>>> b. Use the imaging insertion pipeline
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets>
>>>>>>>>>>> to load your DICOMs.
>>>>>>>>>>> You will want to first ensure that the PatientName header in the
>>>>>>>>>>> DICOMs as well as tar package are correctly labelled with
>>>>>>>>>>> PSCID_DCCID_VisitLabel
>>>>>>>>>>>
>>>>>>>>>>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>> How to :
>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>
>>>>>>>>>>> Be sure to use the *-c* and *-s* options when running the
>>>>>>>>>>> bids_import script, to automatically create your candidates and
>>>>>>>>>>> sessions.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> How do i delete a Study? And everytime do i have to create a new
>>>>>>>>>>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>
>>>>>>>>>>> *First execution:*
>>>>>>>>>>>
>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>> DBD::mysql::db do failed: Cannot add or update a child row: a
>>>>>>>>>>> foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT
>>>>>>>>>>> `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>>>>>>>>>> (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>> ERROR: Failed to insert record in table mri_scanner:
>>>>>>>>>>> The following database commands failed:
>>>>>>>>>>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>> SET
>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>> Medical Systems';
>>>>>>>>>>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>> Error obtained:Cannot add or update a child row: a foreign key
>>>>>>>>>>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>
>>>>>>>>>>> ERROR: The validation has failed. Either re-run the validation
>>>>>>>>>>> again and fix the problem. Or re-run tarchiveLoader.pl using -force to
>>>>>>>>>>> force the execution.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> *And second execution: *
>>>>>>>>>>>
>>>>>>>>>>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>> ./batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>
>>>>>>>>>>> PROBLEM:
>>>>>>>>>>> The user 'lorisadmin' has already inserted this study.
>>>>>>>>>>> The unique study ID is
>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>> This is the information retained from the first time the study
>>>>>>>>>>> was inserted:
>>>>>>>>>>>
>>>>>>>>>>> * Taken from dir :
>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>> * Archive target location :
>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>> * Name of creating host : 127.0.1.1
>>>>>>>>>>> * Name of host OS : Linux
>>>>>>>>>>> * Created by user : lorisadmin
>>>>>>>>>>> * Archived on : 2019-09-04 18:33:05
>>>>>>>>>>> * dicomSummary version : 1
>>>>>>>>>>> * dicomTar version : 1
>>>>>>>>>>> * md5sum for DICOM tarball :
>>>>>>>>>>> 4a301b0318178b09b91e63544282364d ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>> * md5sum for complete archive :
>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Last update of record:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> The dicomTar.pl execution has failed.
>>>>>>>>>>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>>>>>>> print() on closed filehandle MAIL at ./
>>>>>>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>>>>>>
>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Ok, this sounds like good progress. Let us know when you next
>>>>>>>>>>> encounter issues as you progress through the Imaging
>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>
>>>>>>>>>>> .
>>>>>>>>>>> I'll look into how we can better handle the incoming/ directory
>>>>>>>>>>> next time.
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>> is populated correctly except its port is 'port' : ''. Also i have
>>>>>>>>>>> tested that i can connect to MySQL with lorisuser.
>>>>>>>>>>>
>>>>>>>>>>> I executed the script again, because the only error i had
>>>>>>>>>>> previously was that the /data/incoming folder didn't exist and there are no
>>>>>>>>>>> errors reported back except of warnings <<mysql: [Warning] Using a password
>>>>>>>>>>> on the command line interface can be insecure>>.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> It's possible -- if the script was unable to connect to the
>>>>>>>>>>> database during its execution (e.g. typo in the password), that would
>>>>>>>>>>> explain the underpopulated Image path and Loris-MRI code path you saw in
>>>>>>>>>>> the Config module.
>>>>>>>>>>> It's hard to tell without seeing the output from your script run
>>>>>>>>>>> -- Did you see a sign of any such error?
>>>>>>>>>>> The Config fields are populated by the imaging_install.sh script
>>>>>>>>>>> (starting at line 222
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222>
>>>>>>>>>>> )
>>>>>>>>>>>
>>>>>>>>>>> For example, check if the database connection information was
>>>>>>>>>>> populated accurately in $mridir
>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>
>>>>>>>>>>> If you are referring to the imaging_install.sh here is an image
>>>>>>>>>>> with the configurations i typed. Maybe the problem is somewhere at the last
>>>>>>>>>>> part which asks to configure as much as possible automatically?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> Glad to hear your LORIS core install is up and working and all
>>>>>>>>>>> the front-end pages are loading.
>>>>>>>>>>>
>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project
>>>>>>>>>>> > and the web interface worked.
>>>>>>>>>>>
>>>>>>>>>>> Yes, it's important that project/ have 775 permissions and that
>>>>>>>>>>> lorisadmin be part of the sudoers group, per step 1 in the
>>>>>>>>>>> install Readme <https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>
>>>>>>>>>>> > As for the Paths, LORIS-MRI code and Image should change LORIS
>>>>>>>>>>> to loris, right?
>>>>>>>>>>>
>>>>>>>>>>> These imaging paths will be updated during your imaging
>>>>>>>>>>> installation <https://github.com/aces/Loris/wiki/Setup> by an
>>>>>>>>>>> automated script -- you do not need to set them manually via the Config
>>>>>>>>>>> module.
>>>>>>>>>>> Please continue to follow the Setup Guide
>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Setup> for detailed steps
>>>>>>>>>>> to follow.
>>>>>>>>>>>
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>> As for the Paths, LORIS-MRI code and Image should change LORIS
>>>>>>>>>>> to loris, right?
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios
>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> i used
>>>>>>>>>>>
>>>>>>>>>>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
>>>>>>>>>>> sudo apt-get install -y nodejs
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> you had suggested in the past, make worked and now i can see all
>>>>>>>>>>> the contents in the web-interface, but i don't need make install?
>>>>>>>>>>>
>>>>>>>>>>> Thanks
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>> Montreal Neurological Institute
>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>> Loris-dev mailing list
>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> christine.rogers at mcgill.ca
>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>> Montreal Neurological Institute
>>>>> McGill University | Montreal | Canada
>>>>>
>>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>
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